1DFQ

THE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH SIALIC ACID

PDB DOI: https://doi.org/10.2210/pdb1DFQ/pdb

Classification: TOXIN
Organism(s): Clostridium tetani
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1999-11-20 Released: 2000-03-24
Deposition Author(s): Emsley, P., Fotinou, C., Black, I., Fairweather, N.F., Charles, I.G., Watts, C., Hewitt, E., Isaacs, N.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.313
R-Value Work: 0.200
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The structures of the H(C) fragment of tetanus toxin with carbohydrate subunit complexes provide insight into ganglioside binding.

Emsley, P., Fotinou, C., Black, I., Fairweather, N.F., Charles, I.G., Watts, C., Hewitt, E., Isaacs, N.W.

(2000) J Biol Chem 275: 8889-8894

PubMed: 10722735 Search on PubMed
DOI: https://doi.org/10.1074/jbc.275.12.8889
Primary Citation of Related Structures:
1D0H, 1DFQ, 1DIW, 1DLL

PubMed Abstract:
The entry of tetanus neurotoxin into neuronal cells proceeds through the initial binding of the toxin to gangliosides on the cell surface. The carboxyl-terminal fragment of the heavy chain of tetanus neurotoxin contains the ganglioside-binding site, which has not yet been fully characterized. The crystal structures of native H(C) and of H(C) soaked with carbohydrates reveal a number of binding sites and provide insight into the possible mode of ganglioside binding.

Organizational Affiliation

Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom.

Macromolecule Content

Total Structure Weight: 51.14 kDa
Atom Count: 3,805
Modelled Residue Count: 441
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TETANUS TOXIN HC	A	444	Clostridium tetani	Mutation(s): 0 EC: 3.4.24.68
UniProt
Find proteins for P04958 (Clostridium tetani (strain Massachusetts / E88)) Explore P04958 Go to UniProtKB: P04958
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04958
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SLB Query on SLB Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-acetyl-beta-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-PFQGKNLYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.313
R-Value Work: 0.200
R-Value Observed: 0.200
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.86	α = 90
b = 70.24	β = 90
c = 122.52	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2000-03-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-03-24
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2024-02-07
Changes: Data collection, Database references, Structure summary